collapsing samples using the median
AnnaC
Hello everyone,
When I perform collapse samples using the median values, I get a lower number of reads than expected. I thought that median value per OTU and category were calculated and then added up to make the total count, but it looks like I am wrong.
Could anyone clarify me that?
Thank you!
I attach different biom summarize tables to show that:
Non-collapsed table begins like this (so I was expecting median values around 40,000 reads).
Num samples: 306
Num observations: 1396
Total count: 13963032
Table density (fraction of non-zero values): 0.275
Counts/sample summary:
Min: 5.0
Max: 191411.0
Median: 41071.000
Mean: 45630.824
Std. dev.: 25281.454
Sample Metadata Categories: None provided
Observation Metadata Categories: taxonomy
This is my biom_summarize when using median values.
Num samples: 35
Num observations: 1396
Total count: 421190
Table density (fraction of non-zero values): 0.260
Counts/sample summary:
Min: 866.5
Max: 22721.5
Median: 12193.000
Mean: 12034.000
Std. dev.: 5978.280
Sample Metadata Categories: collapsed_ids
Observation Metadata Categories: taxonomy
Counts/sample detail:
16: 866.5
15: 1405.0
7: 3076.0
4: 3808.5
34: 4245.0
2: 5493.5
25: 6203.0
36: 6531.5
32: 6626.5
12: 7568.0
1: 8692.0
35: 9542.5
17: 9898.0
30: 9906.0
3: 10953.5
14: 11353.0
33: 11573.0
20: 12193.0
24: 12431.5
11: 13303.5
8: 13645.0
29: 13858.0
28: 13986.5
5: 15144.0
6: 15161.0
9: 15919.5
19: 16498.5
27: 17292.0
21: 18055.0
18: 19289.0
13: 20035.0
22: 20362.5
26: 21552.0
31: 22001.0
23: 22721.5
